GENETICS - Biology 311
Fall 2015 Syllabus
Contact Information
Instructor:
Office:
Phone:
E-mail:
Research Lab:
Dr. Bryan Thines
Thompson Hall 223G
(253) 879-3797
bthines@pugetsound.edu
Thompson Hall 220
Class Meeting Times: M W F, 10 – 10:50am
Office Hours: M 11 – 11:50am, R 9 – 9:50am, plus scheduled recitation (see below)
Introduction
The 21st century is the most exciting time to study Genetics. Though we have had
models for heredity since the mid-1800s and we have known about the structure of DNA
since the 1950s, in only the last few years our genome sequencing capabilities have
revolutionized the field of genetics. Consequences of this revolution are far-reaching
and diverse fields are impacted, ranging from precision medicine to conservation
biology. New ethical issues have arisen concomitantly with the unprecedented ability to
gather and archive genetic information. In this class we will focus on and apply core
concepts of modern genetics. We will also discuss modern methodologies related to
this field and critical interpretation of data generated by these approaches.
Course Objectives
The primary objective of this course is for you to develop an understanding of genetics
concepts. In this course, you will:
1. Think logically and critically as you apply genetics concepts to analyze and solve
problems
2. Collect, interpret, and present scientific data gained through experimentation
3. Communicate your ideas effectively through writing
4. Relate genetics concepts to your own experience as an individual and as a
member of society
1 Textbook
Genetics: A Conceptual Approach, 5th ed., B.A. Pierce, 2014
Additional readings and laboratory protocols will be posted on Moodle
Contacting the Instructor
E-mails: I do not answer e-mails after 5:30pm on weekdays, but I will respond first
thing the next morning if you e-mail after this time. I will answer any weekend e-mails
by Sunday evening. If you have questions about class, lab, careers, or just about
anything else, it is best to come and talk to me in person. I have an open door
policy, and you are welcome to come talk to me at almost any time.
Class Procedures
Attendance during lecture is required. Please be on time.
ALL lecture and lab materials will be posted on Moodle. A lecture guide for the
coming week will be posted every Friday evening. This guide will contain a list of
topics and learning objectives for the coming week and should be reviewed ahead of
lecture. I strongly recommend reading the textbook ahead of time with the lecture guide
in hand. I will also post Powerpoint slides and any additional materials that we use in
class on Moodle immediately following lectures.
Recitation
My goal is to give you the support you need to be successful in this course.
Recitation is a time for us to meet as a group to review and discuss topics covered in
class. In my experience, students often have similar questions during office hours, and
addressing these questions with everyone present leads to a more in-depth and
meaningful discussion. Group discussion often leads to other questions that you may
not realize you had. Recitation is also a time to work on practice problems and to
prepare for exams. No new material will be covered during recitation, and any materials
that I bring to recitation (ie. practice problems) I will bring also to the next class. During
the second week of class, I will schedule one or two regular recitation times depending
on your schedule. Participation in recitation is optional, but I highly recommend
attending this activity.
2 Required Work and Assessment of Learning
The class components below will be worth the following percentages of your total grade:
Exams (two mid-terms and final) 60%
Blog
20%
Lab (including report)
20%
Grading scale:
93-100% A
90-92% A87-89% B+
83-86% B
80-82% B77-79% C+
73-76% C
70-72% C67-69% D+
63-66% D
60-62% D<60% F
Blog Assignment: information will be provided during second week of class
Exams: a take home portion of each exam will be given the week prior to the in-class
portion. Any material covered in class is fair game for the exam, and not all material we
cover may be in the textbook (so, come to class and be on time!).
The final exam is on: Friday December 18th from 8am to 10am
Lab: additional information will be provided on your first day of lab
Laboratory
Through the laboratory portion of this course you will learn some of the techniques and
skills used in genetic research as well as apply concepts covered in class. The
laboratory schedule will be provided on the first day of lab and is available on Moodle.
Laboratory protocols and exercises are posted on Moodle. Please read the lab
materials and prepare for lab well in advance. Some lab protocols require you to
prepare components of the lab one or two days prior to your scheduled lab time. Bring
the protocol(s) to lab—you may bring your laptop, electronic device, or a paper copy of
the lab protocols; or you may write the protocol in your lab notebook (see below).
Please purchase a lab notebook prior to the first lab session. The notebook can be a
composition book (graph paper pages are recommended) or a spiral-bound notebook.
The notebook does not need to have carbon copy pages. The laboratory component of
this course will include multi-week experiments. We will use two eukaryotic model
organisms for these experiments: Drosophila melanogaster (fruit flies) and
3 Saccharomyces cerevisiae (brewer’s or baker’s yeast). Using live organisms introduces
variability; so while you are encouraged to look ahead at documents for future labs, be
aware that the lab protocols and lab schedule may vary throughout the semester.
You will write one laboratory report during the semester; detailed instructions about the
format will be provided in lab.
Academic Integrity
The university’s academic integrity policy is clear and comprehensive. It is available
online [http://www.pugetsound.edu/student-life/student-resources/studenthandbook/academic- handbook/academic-integrity/] and in the printed Academic
Handbook. You are responsible for understanding what constitutes plagiarism and
other forms of academic dishonesty. If you have a question as to whether
something constitutes plagiarism, ask! Academic integrity is vital to your work as a
student, including in this course. Cheating, plagiarism, and other forms of academic
dishonesty will NOT be tolerated. Contact me with any other questions regarding
academic integrity.
Behavior Expectations
I expect you to behave in an appropriate manner while attending this class. Use your
common sense, but here are a few guidelines:
Be punctual—be on time for both class and lab.
During class and lab I expect you to be working on materials for this course only.
Personal technology--please be respectful of others in class:
Switch your phone off before coming to class. Refrain from using email or
text messaging during class. You may not touch or use your
phone/laptop/tablet in any way during an exam. You may not listen to an
iPod, phone, or similar device during class or during an exam
You may not make audio recordings of our class or lab sessions without prior
consent from me.
If you leave the room during an exam, your paper will be collected and you will
not be permitted to return to the exam.
Lack of respect for diversity will not be tolerated in the class. Diversity
encompasses age, life experiences, profession, race, religion, gender, lifestyle,
social class, learning style, ethnicity, philosophy of life, sexual orientation,
personality, mental and physical challenges, customs, and values, among others.
You may bring food and/or drinks to class as long as the consumption of food
and/or drinks is not a distraction to others.
4 ABSOLUTELY NO FOOD OR DRINK is allowed in the laboratory. Food and/or
drinks can be kept outside the lab door. Wash your hands prior to consuming
food or drink.
Telephones located in classrooms and labs are for staff use and medical/safety
emergencies only (no personal calls).
Bereavement Policy
Upon approval from the Dean of Students’ Office, students who experience a death in
the family, including parent, grandparent, sibling, or persons living in the same
household, are allowed three consecutive weekdays of excused absences, as
negotiated with the Dean of Students. For more information, please see the Academic
Handbook.
Accessibility and Accommodation
If you have a physical, psychological, medical or learning disability that may impact your
course work, please contact Peggy Perno, Director of the Office of Accessibility and
Accommodation, 105 Howarth (253.879.3395). She will determine with you what
accommodations are necessary and appropriate. All information and documentation is
confidential. Please notify me well in advance should you require accommodation in the
class or lab.
Emergency Response Procedures
Please review university emergency preparedness and response procedures posted at
www.pugetsound.edu/emergency/. There is a link on the university home page.
Familiarize yourself with hall exit doors and the designated gathering area for your class
and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the
designated gathering area so she/he can account for your presence. Then wait for
further instructions. Do not return to the building or classroom until advised by a
university emergency response representative. If confronted by an act of violence, be
prepared to make quick decisions to protect your safety. Flee the area by running away
from the source of danger only if you can safely do so. If this is not possible, shelter in
place by securing classroom or lab doors and windows, closing blinds, and turning off
room lights. Lie on the floor out of sight and away from windows and doors. Place cell
phones or pagers on vibrate so that you can receive messages quietly. Wait for further
instructions.
5 Schedule
(Note: this schedule is tentative and subject to change)
DATE TOPIC CHAPTER ASSIGNMENTS Aug. 31 Sept. 2 4 9 11 14 16 18 21 23 25 28 30 Oct. 2 5 7 9 12 14 16 21 23 26 28 30 Nov. 2 4 6 9 11 13 16 18 20 23 30 Dec. 2 4 7 Introduction; Current Topics in Personal Genomics Structure of DNA DNA and Chromosomes DNA Replication DNA Replication What is a Gene? Transcription Transcription RNA Processing RNA Processing Genetic Code and Translation Genetic Code and Translation Paper Discussion Regulation of Genes in Prokaryotes Regulation of Genes in Prokaryotes Exam 1 Regulation of genes in Eukaryotes Regulation of genes in Eukaryotes Molecular Understanding of Mutation Molecular Understanding of Mutation Molecular Understanding of Mutation Chromosomes and Cellular Reproduction Chromosomes and Cellular Reproduction Mendelian Genetics Mendelian Genetics Sex Chromosomes Paper Discussion Mendelian Genetics (modifications/extensions) Mendelian Genetics (modifications/extensions) Exam 2 Pedigree Analysis and Human Genetics Mapping Genes Mapping Genes Epigenetics Epigenetics Quantitative Genetics Quantitative Genetics Paper Discussion Population Genetics 10 11 12 12 14 13 13 14 14 15 15 16 16 24 24 25 Blog -­‐ paper selection due Take home exam question distributed Blog -­‐ additional references due Blog -­‐ figures due Blog -­‐ draft 1 due Take home exam question distributed Blog -­‐ draft 2 due Blog -­‐ reviews due Blog -­‐ final version 25 Take home exam question distributed 9 Population Genetics 17 17 18 18 18 2 2 3 3 4 5 5 6 7 7 21 6 7